feat: add support for reading unit cell dimensions from @<TRIPOS>CRYSIN records in MOL2Parser

Author: Dreamstick9

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
-         spyke7, talagayev
+         spyke7, talagayev, Dreamstick9
 
  * 2.11.0
 
@@ -28,6 +28,7 @@ Fixes
    to version 5.1.0 (Issue #5145, PR #5146)
  * Fixes incorrect assignment of secondary structure to proline residues in
    DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
+ * MOL2Parser now reads unit cell dimensions from @<TRIPOS>CRYSIN records (Issue #3341)
 
 Enhancements
  * Enables parallelization for analysis.diffusionmap.DistanceMatrix
@@ -223,7 +224,6 @@ Fixes
  * Fix doctest errors of lib/picklable_file_io.py (Issue #3925, PR #4371)
  * Fix deploy action to use the correct version of the pypi upload action.
  * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
- * MOL2Parser now reads unit cell dimensions from @<TRIPOS>CRYSIN records (Issue #3341)
 
 Enhancements
  * Removed type and mass guessing from all topology parsers (PR #3753)

package/MDAnalysis/coordinates/MOL2.py

@@ -69,8 +69,11 @@
 * The MDAnalysis :class:`MOL2Reader` and :class:`MOL2Writer` only handle the
   MOLECULE, SUBSTRUCTURE, ATOM, and BOND record types. Other records are not
   currently read or preserved on writing.
-* As the CRYSIN record type is not parsed / written, MOL2 systems always have
-  dimensions set to ``None`` and dimensionless MOL2 files are written.
+* The MDAnalysis :class:`MOL2Reader` now reads unit cell dimensions from the
+  @<TRIPOS>CRYSIN record. The space group and setting information (the 7th
+  and 8th fields) are currently ignored. The unit cell is interpreted in the
+  common crystallographic convention with box vector **a** parallel to the x-axis,
+  **b** in the xy-plane, and **c** having a positive z-component.
 
 
 MOL2 format notes
@@ -247,12 +250,9 @@ def _read_frame(self, frame):
             except KeyError:
                 pass
         if "crysin" in sections:
-            try:
-                line = sections["crysin"][0].strip()
-                dims = [float(x) for x in line.split()[:6]]
-                self.ts.dimensions = np.array(dims, dtype=np.float32)
-            except (ValueError, IndexError):
-                pass
+            line = sections["crysin"][0].strip()
+            dims = [float(x) for x in line.split()[:6]]
+            self.ts.dimensions = np.array(dims, dtype=np.float32)
 
         self.ts.positions = np.array(coords, dtype=np.float32)